Sequence
atgc intronic sequence ATGC exonic sequencegtgagattaagagcctaactatagagtctttttacttcatttcagAAAGAGCTTGAAGCCGAGATGAAAAGATTGAGGCTTGAACTGAAGCAAACTATGGACATGTACAGCTCAGCTTGCAAGCAAGCAATCTCAGCCAAAAATC
Basic information
species | Glycine max |
transcript | GLYMA04G05600.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G05600.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------gtgagattaagagcctaactatagagtctttttacttcatttcagAAAGAGCTTGAAGCCGAGATGAAAAGATTGAGGCTTGAACTGAAGCAAACTATGGACATGTACAGCTCAGCTTGCAAGCAAGCAATCTCAGCCAAAAATC
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gtatgtaaacaagtagagcaatagactttatgatgatatcgagtttgataagattagtatgc--actaaattggttggatttttatttgcagAGGGATATTGAAGCTGAGATGAAAAGGTTAAAGATTGAACTCAAGCAAACCATGGACATGTATAGCTCAGCCTGCAAAGAAGCACTTAATGCAAAAAAGA
upper sequence: GLYMA04G05600.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G26150.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------gtgagattaagag--cctaactatagagtc--tttttacttcattt-cagAAAGAGCTTGAAGCCGAGATGAAAAGATTGAGGCTTGAACTGAAGCAAACTATGGACATGTACAGCTCAGCTTGCAAGCAAGCAATCTCAGCCAAAAATC
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gtacgttttcttgaacgaatttctttttaggttcaagaattaagtttgaaaggctctaaatgtaaatatggttgttgctttatttgcagAAAGATATTGAAGCTGAGATGAGAAGGCTAAAGCTTGAACTTAAGCAAACTATGGACATGTATAGCTCAGCTTGTAAAGAAGCACTTACGGCAAAAAGAA
upper sequence: GLYMA04G05600.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0008g01360.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------gtgagattaagag------cctaactatagagtctttttacttcatttcagAAAGAGCTTGAAGCCGAGATGAAAAGATTGAGGCTTGAACTGAAGCAAACTATGGACATGTACAGCTCAGCTTGCAAGCAAGCAATCTCAGCCAAAAATC
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gtaagtgaaaattttatgagaagtgaggaaattcagtgaagttatctgatttgatcatgtgttgattcatttacagAAAGAATTAGCTGCTGAGATGAAAAGATTAAAGCTTGAACTGAAGCAAACCATGGACATGTACAGCACAGCTTGCAAAGAAGCAATAACAGCTAAACAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgagattaagagcctaactatagagtctttttacttcatttcagAAAGAGCTTGAAGCCGAGATGAAAAGATTGAGGCTTGAACTGAAGCAAACTATGGACATGTACAGCTCAGCTTGCAAGCAAGCAATCTCAGCCAAAAATC
gcctaac putative branch site (score: 2)
tctttttacttcattt putative PPT
tttttacttcattt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagattaagagcctaactatagagtctttttacttcatttcagAAAGAGCTTGAAGCCGAGATGAAAAGATTGAGGCTTGAACTGAAGCAAACTATGGACATGTACAGCTCAGCTTGCAAGCAAGCAATCTCAGCCAAAAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA